Multiple sequence alignment - TraesCS4D01G092400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4D01G092400 chr4D 100.000 2561 0 0 1 2561 67327189 67324629 0.000000e+00 4730.0
1 TraesCS4D01G092400 chr4D 82.979 188 22 8 2373 2551 473832679 473832493 7.330000e-36 161.0
2 TraesCS4D01G092400 chr4A 90.117 2054 148 22 546 2561 516582831 516584867 0.000000e+00 2617.0
3 TraesCS4D01G092400 chr4A 80.856 794 119 16 813 1584 641443081 641442299 6.100000e-166 593.0
4 TraesCS4D01G092400 chr4A 94.624 93 5 0 29 121 516581460 516581552 7.390000e-31 145.0
5 TraesCS4D01G092400 chr4B 88.256 2018 162 32 589 2561 99593705 99595692 0.000000e+00 2344.0
6 TraesCS4D01G092400 chr5D 79.844 769 123 19 813 1570 530834507 530835254 1.350000e-147 532.0
7 TraesCS4D01G092400 chr5D 86.806 144 15 4 2370 2510 431400315 431400457 9.490000e-35 158.0
8 TraesCS4D01G092400 chr5B 79.028 782 128 24 813 1582 670074466 670075223 1.060000e-138 503.0
9 TraesCS4D01G092400 chr5B 87.912 91 11 0 374 464 633982394 633982484 9.690000e-20 108.0
10 TraesCS4D01G092400 chr2D 90.698 129 8 4 2373 2497 620523095 620522967 4.380000e-38 169.0
11 TraesCS4D01G092400 chr3B 81.773 203 23 7 2369 2558 680220077 680220278 9.490000e-35 158.0
12 TraesCS4D01G092400 chr7B 87.970 133 8 6 2372 2499 636935660 636935531 1.590000e-32 150.0
13 TraesCS4D01G092400 chr1B 81.000 200 29 9 2367 2558 668003714 668003516 1.590000e-32 150.0
14 TraesCS4D01G092400 chr6B 86.429 140 14 5 2361 2496 642730777 642730915 5.710000e-32 148.0
15 TraesCS4D01G092400 chr6B 83.562 73 9 3 397 466 158128903 158128975 5.910000e-07 65.8
16 TraesCS4D01G092400 chr2B 81.218 197 24 12 2373 2558 151646097 151645903 2.050000e-31 147.0
17 TraesCS4D01G092400 chr6A 79.803 203 21 12 2373 2558 111564390 111564191 2.070000e-26 130.0
18 TraesCS4D01G092400 chr7A 88.043 92 11 0 373 464 68193192 68193101 2.690000e-20 110.0
19 TraesCS4D01G092400 chr3A 88.764 89 10 0 379 467 712549315 712549403 2.690000e-20 110.0
20 TraesCS4D01G092400 chr7D 86.170 94 13 0 373 466 12909814 12909721 4.510000e-18 102.0
21 TraesCS4D01G092400 chr7D 83.673 98 15 1 373 469 82790457 82790554 9.760000e-15 91.6
22 TraesCS4D01G092400 chr3D 86.170 94 13 0 373 466 133111639 133111546 4.510000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G092400 chr4D 67324629 67327189 2560 True 4730 4730 100.0000 1 2561 1 chr4D.!!$R1 2560
1 TraesCS4D01G092400 chr4A 516581460 516584867 3407 False 1381 2617 92.3705 29 2561 2 chr4A.!!$F1 2532
2 TraesCS4D01G092400 chr4A 641442299 641443081 782 True 593 593 80.8560 813 1584 1 chr4A.!!$R1 771
3 TraesCS4D01G092400 chr4B 99593705 99595692 1987 False 2344 2344 88.2560 589 2561 1 chr4B.!!$F1 1972
4 TraesCS4D01G092400 chr5D 530834507 530835254 747 False 532 532 79.8440 813 1570 1 chr5D.!!$F2 757
5 TraesCS4D01G092400 chr5B 670074466 670075223 757 False 503 503 79.0280 813 1582 1 chr5B.!!$F2 769

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
301 302 0.175073 GTCATAACGCTCGTTCCCCT 59.825 55.0 11.14 0.0 39.31 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1686 2751 0.687427 AACCCAAGCAAAGGCACACT 60.687 50.0 0.0 0.0 44.61 3.55 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 5.623956 TCATACAGTTGGGGTTCGATAAT 57.376 39.130 0.00 0.00 0.00 1.28
55 56 3.063452 CAGTTGGGGTTCGATAATTCACG 59.937 47.826 0.00 0.00 0.00 4.35
81 82 4.213270 CCGTTTGTTTACATCTCAGAGCAA 59.787 41.667 0.00 0.00 0.00 3.91
88 89 1.138661 ACATCTCAGAGCAAGCCTAGC 59.861 52.381 0.00 0.00 0.00 3.42
138 139 3.680777 GGGACCCCTATGGAAATTGAA 57.319 47.619 0.00 0.00 38.00 2.69
139 140 3.296854 GGGACCCCTATGGAAATTGAAC 58.703 50.000 0.00 0.00 38.00 3.18
140 141 2.949644 GGACCCCTATGGAAATTGAACG 59.050 50.000 0.00 0.00 38.00 3.95
141 142 2.949644 GACCCCTATGGAAATTGAACGG 59.050 50.000 0.00 0.00 38.00 4.44
142 143 2.310647 ACCCCTATGGAAATTGAACGGT 59.689 45.455 0.00 0.00 38.00 4.83
143 144 3.245479 ACCCCTATGGAAATTGAACGGTT 60.245 43.478 0.00 0.00 38.00 4.44
144 145 3.767131 CCCCTATGGAAATTGAACGGTTT 59.233 43.478 0.00 0.00 35.39 3.27
145 146 4.221924 CCCCTATGGAAATTGAACGGTTTT 59.778 41.667 0.00 0.00 35.39 2.43
146 147 5.407502 CCCTATGGAAATTGAACGGTTTTC 58.592 41.667 0.00 0.00 0.00 2.29
147 148 5.407502 CCTATGGAAATTGAACGGTTTTCC 58.592 41.667 12.89 12.89 45.59 3.13
148 149 5.185056 CCTATGGAAATTGAACGGTTTTCCT 59.815 40.000 18.09 9.70 45.59 3.36
149 150 4.314740 TGGAAATTGAACGGTTTTCCTG 57.685 40.909 18.09 0.00 45.59 3.86
150 151 3.702045 TGGAAATTGAACGGTTTTCCTGT 59.298 39.130 18.09 0.00 45.59 4.00
151 152 4.048504 GGAAATTGAACGGTTTTCCTGTG 58.951 43.478 12.62 0.00 43.24 3.66
152 153 4.202070 GGAAATTGAACGGTTTTCCTGTGA 60.202 41.667 12.62 0.00 43.24 3.58
153 154 4.993029 AATTGAACGGTTTTCCTGTGAA 57.007 36.364 0.00 0.00 37.95 3.18
154 155 4.993029 ATTGAACGGTTTTCCTGTGAAA 57.007 36.364 0.00 0.00 38.69 2.69
155 156 3.768468 TGAACGGTTTTCCTGTGAAAC 57.232 42.857 0.00 0.00 40.12 2.78
157 158 3.119779 TGAACGGTTTTCCTGTGAAACAC 60.120 43.478 0.00 0.00 45.67 3.32
158 159 1.746787 ACGGTTTTCCTGTGAAACACC 59.253 47.619 0.00 0.00 45.67 4.16
159 160 1.066454 CGGTTTTCCTGTGAAACACCC 59.934 52.381 0.00 0.00 45.67 4.61
160 161 1.066454 GGTTTTCCTGTGAAACACCCG 59.934 52.381 0.00 0.00 45.67 5.28
161 162 1.066454 GTTTTCCTGTGAAACACCCGG 59.934 52.381 0.00 0.00 45.67 5.73
162 163 0.466555 TTTCCTGTGAAACACCCGGG 60.467 55.000 22.25 22.25 45.67 5.73
163 164 2.282180 CCTGTGAAACACCCGGGG 60.282 66.667 27.92 16.65 45.67 5.73
164 165 2.983592 CTGTGAAACACCCGGGGC 60.984 66.667 27.92 9.04 45.67 5.80
165 166 3.783362 CTGTGAAACACCCGGGGCA 62.783 63.158 27.92 11.76 45.67 5.36
196 197 2.049228 CGGTTCGCGGTATGATAACTC 58.951 52.381 6.13 0.00 0.00 3.01
206 207 4.500887 CGGTATGATAACTCGTGGACCATT 60.501 45.833 0.00 0.00 0.00 3.16
211 212 5.795972 TGATAACTCGTGGACCATTTGTTA 58.204 37.500 14.28 14.28 0.00 2.41
212 213 5.640357 TGATAACTCGTGGACCATTTGTTAC 59.360 40.000 14.24 10.65 0.00 2.50
213 214 3.764237 ACTCGTGGACCATTTGTTACT 57.236 42.857 0.00 0.00 0.00 2.24
214 215 3.660865 ACTCGTGGACCATTTGTTACTC 58.339 45.455 0.00 0.00 0.00 2.59
215 216 3.000727 CTCGTGGACCATTTGTTACTCC 58.999 50.000 0.00 0.00 0.00 3.85
216 217 2.635915 TCGTGGACCATTTGTTACTCCT 59.364 45.455 0.00 0.00 0.00 3.69
217 218 3.000727 CGTGGACCATTTGTTACTCCTC 58.999 50.000 0.00 0.00 0.00 3.71
218 219 3.556213 CGTGGACCATTTGTTACTCCTCA 60.556 47.826 0.00 0.00 0.00 3.86
219 220 4.589908 GTGGACCATTTGTTACTCCTCAT 58.410 43.478 0.00 0.00 0.00 2.90
220 221 4.396166 GTGGACCATTTGTTACTCCTCATG 59.604 45.833 0.00 0.00 0.00 3.07
221 222 4.042809 TGGACCATTTGTTACTCCTCATGT 59.957 41.667 0.00 0.00 0.00 3.21
222 223 4.636206 GGACCATTTGTTACTCCTCATGTC 59.364 45.833 0.00 0.00 0.00 3.06
223 224 4.589908 ACCATTTGTTACTCCTCATGTCC 58.410 43.478 0.00 0.00 0.00 4.02
224 225 3.623060 CCATTTGTTACTCCTCATGTCCG 59.377 47.826 0.00 0.00 0.00 4.79
225 226 3.328382 TTTGTTACTCCTCATGTCCGG 57.672 47.619 0.00 0.00 0.00 5.14
226 227 2.225382 TGTTACTCCTCATGTCCGGA 57.775 50.000 0.00 0.00 0.00 5.14
234 235 4.402056 TCCTCATGTCCGGAGATTTTAC 57.598 45.455 12.20 0.00 34.24 2.01
235 236 4.030913 TCCTCATGTCCGGAGATTTTACT 58.969 43.478 12.20 0.00 34.24 2.24
236 237 4.469945 TCCTCATGTCCGGAGATTTTACTT 59.530 41.667 12.20 0.00 34.24 2.24
237 238 5.045869 TCCTCATGTCCGGAGATTTTACTTT 60.046 40.000 12.20 0.00 34.24 2.66
238 239 6.155565 TCCTCATGTCCGGAGATTTTACTTTA 59.844 38.462 12.20 0.00 34.24 1.85
239 240 6.992715 CCTCATGTCCGGAGATTTTACTTTAT 59.007 38.462 12.20 0.00 34.24 1.40
263 264 4.176271 GCCTAAAATGTCAGCAAATCCAC 58.824 43.478 0.00 0.00 0.00 4.02
275 276 2.159338 GCAAATCCACCATGCACACTAG 60.159 50.000 0.00 0.00 39.81 2.57
286 287 4.363138 CATGCACACTAGTCATACGTCAT 58.637 43.478 0.00 0.00 0.00 3.06
301 302 0.175073 GTCATAACGCTCGTTCCCCT 59.825 55.000 11.14 0.00 39.31 4.79
302 303 1.406539 GTCATAACGCTCGTTCCCCTA 59.593 52.381 11.14 0.00 39.31 3.53
329 330 2.481441 AGTCATAATGCTCCAGGTCCA 58.519 47.619 0.00 0.00 0.00 4.02
339 340 3.245586 TGCTCCAGGTCCAATGGTAAAAT 60.246 43.478 0.00 0.00 39.01 1.82
356 357 9.677567 ATGGTAAAATGCTTACTTAATATTGCG 57.322 29.630 0.00 0.00 0.00 4.85
371 372 1.237533 TTGCGCGCCATGATTATCAT 58.762 45.000 30.77 1.25 37.65 2.45
372 373 1.237533 TGCGCGCCATGATTATCATT 58.762 45.000 30.77 0.00 34.28 2.57
373 374 1.608109 TGCGCGCCATGATTATCATTT 59.392 42.857 30.77 0.00 34.28 2.32
374 375 2.034432 TGCGCGCCATGATTATCATTTT 59.966 40.909 30.77 0.00 34.28 1.82
375 376 3.052036 GCGCGCCATGATTATCATTTTT 58.948 40.909 23.24 0.00 34.28 1.94
404 405 9.379791 AGAGGGTTACTTCTTTATTTTGTATCG 57.620 33.333 0.00 0.00 0.00 2.92
405 406 9.159364 GAGGGTTACTTCTTTATTTTGTATCGT 57.841 33.333 0.00 0.00 0.00 3.73
406 407 9.511272 AGGGTTACTTCTTTATTTTGTATCGTT 57.489 29.630 0.00 0.00 0.00 3.85
407 408 9.764870 GGGTTACTTCTTTATTTTGTATCGTTC 57.235 33.333 0.00 0.00 0.00 3.95
408 409 9.469239 GGTTACTTCTTTATTTTGTATCGTTCG 57.531 33.333 0.00 0.00 0.00 3.95
409 410 9.469239 GTTACTTCTTTATTTTGTATCGTTCGG 57.531 33.333 0.00 0.00 0.00 4.30
410 411 6.540205 ACTTCTTTATTTTGTATCGTTCGGC 58.460 36.000 0.00 0.00 0.00 5.54
411 412 5.473796 TCTTTATTTTGTATCGTTCGGCC 57.526 39.130 0.00 0.00 0.00 6.13
412 413 3.929417 TTATTTTGTATCGTTCGGCCG 57.071 42.857 22.12 22.12 0.00 6.13
413 414 1.729284 ATTTTGTATCGTTCGGCCGT 58.271 45.000 27.15 7.91 0.00 5.68
414 415 0.791422 TTTTGTATCGTTCGGCCGTG 59.209 50.000 27.15 16.45 0.00 4.94
415 416 0.319727 TTTGTATCGTTCGGCCGTGT 60.320 50.000 27.15 10.18 0.00 4.49
416 417 0.525311 TTGTATCGTTCGGCCGTGTA 59.475 50.000 27.15 9.28 0.00 2.90
417 418 0.740149 TGTATCGTTCGGCCGTGTAT 59.260 50.000 27.15 16.41 0.00 2.29
418 419 1.134753 TGTATCGTTCGGCCGTGTATT 59.865 47.619 27.15 11.29 0.00 1.89
419 420 2.195922 GTATCGTTCGGCCGTGTATTT 58.804 47.619 27.15 9.63 0.00 1.40
420 421 1.729284 ATCGTTCGGCCGTGTATTTT 58.271 45.000 27.15 2.35 0.00 1.82
421 422 0.791422 TCGTTCGGCCGTGTATTTTG 59.209 50.000 27.15 7.72 0.00 2.44
422 423 0.791422 CGTTCGGCCGTGTATTTTGA 59.209 50.000 27.15 0.00 0.00 2.69
423 424 1.395608 CGTTCGGCCGTGTATTTTGAT 59.604 47.619 27.15 0.00 0.00 2.57
424 425 2.159626 CGTTCGGCCGTGTATTTTGATT 60.160 45.455 27.15 0.00 0.00 2.57
425 426 3.168193 GTTCGGCCGTGTATTTTGATTG 58.832 45.455 27.15 0.00 0.00 2.67
426 427 2.428491 TCGGCCGTGTATTTTGATTGT 58.572 42.857 27.15 0.00 0.00 2.71
427 428 2.814919 TCGGCCGTGTATTTTGATTGTT 59.185 40.909 27.15 0.00 0.00 2.83
428 429 2.914214 CGGCCGTGTATTTTGATTGTTG 59.086 45.455 19.50 0.00 0.00 3.33
429 430 3.610585 CGGCCGTGTATTTTGATTGTTGT 60.611 43.478 19.50 0.00 0.00 3.32
430 431 4.303282 GGCCGTGTATTTTGATTGTTGTT 58.697 39.130 0.00 0.00 0.00 2.83
431 432 4.747605 GGCCGTGTATTTTGATTGTTGTTT 59.252 37.500 0.00 0.00 0.00 2.83
432 433 5.235401 GGCCGTGTATTTTGATTGTTGTTTT 59.765 36.000 0.00 0.00 0.00 2.43
433 434 6.421202 GGCCGTGTATTTTGATTGTTGTTTTA 59.579 34.615 0.00 0.00 0.00 1.52
434 435 7.117092 GGCCGTGTATTTTGATTGTTGTTTTAT 59.883 33.333 0.00 0.00 0.00 1.40
435 436 8.159709 GCCGTGTATTTTGATTGTTGTTTTATC 58.840 33.333 0.00 0.00 0.00 1.75
436 437 9.405587 CCGTGTATTTTGATTGTTGTTTTATCT 57.594 29.630 0.00 0.00 0.00 1.98
445 446 9.781834 TTGATTGTTGTTTTATCTATAAAGCGG 57.218 29.630 5.27 0.00 36.59 5.52
446 447 8.402472 TGATTGTTGTTTTATCTATAAAGCGGG 58.598 33.333 5.27 0.00 36.59 6.13
447 448 6.687081 TGTTGTTTTATCTATAAAGCGGGG 57.313 37.500 5.27 0.00 36.59 5.73
448 449 5.066764 TGTTGTTTTATCTATAAAGCGGGGC 59.933 40.000 5.27 0.00 36.59 5.80
449 450 3.810941 TGTTTTATCTATAAAGCGGGGCG 59.189 43.478 5.27 0.00 36.59 6.13
465 466 2.126463 CGCGAGCCTGTTTCGAGA 60.126 61.111 0.00 0.00 39.70 4.04
466 467 2.155194 CGCGAGCCTGTTTCGAGAG 61.155 63.158 0.00 0.00 39.70 3.20
467 468 1.080434 GCGAGCCTGTTTCGAGAGT 60.080 57.895 0.00 0.00 40.36 3.24
468 469 1.347817 GCGAGCCTGTTTCGAGAGTG 61.348 60.000 0.00 0.00 40.36 3.51
469 470 0.241213 CGAGCCTGTTTCGAGAGTGA 59.759 55.000 0.00 0.00 40.36 3.41
470 471 1.730772 CGAGCCTGTTTCGAGAGTGAG 60.731 57.143 0.00 0.00 40.36 3.51
471 472 1.542030 GAGCCTGTTTCGAGAGTGAGA 59.458 52.381 0.00 0.00 0.00 3.27
472 473 2.165437 GAGCCTGTTTCGAGAGTGAGAT 59.835 50.000 0.00 0.00 0.00 2.75
473 474 2.564947 AGCCTGTTTCGAGAGTGAGATT 59.435 45.455 0.00 0.00 0.00 2.40
474 475 3.764434 AGCCTGTTTCGAGAGTGAGATTA 59.236 43.478 0.00 0.00 0.00 1.75
475 476 4.404073 AGCCTGTTTCGAGAGTGAGATTAT 59.596 41.667 0.00 0.00 0.00 1.28
476 477 4.742659 GCCTGTTTCGAGAGTGAGATTATC 59.257 45.833 0.00 0.00 0.00 1.75
477 478 5.679894 GCCTGTTTCGAGAGTGAGATTATCA 60.680 44.000 0.00 0.00 34.79 2.15
478 479 6.511416 CCTGTTTCGAGAGTGAGATTATCAT 58.489 40.000 0.00 0.00 40.92 2.45
479 480 6.983307 CCTGTTTCGAGAGTGAGATTATCATT 59.017 38.462 0.00 0.00 40.92 2.57
490 491 9.875675 GAGTGAGATTATCATTTTTGTCATAGC 57.124 33.333 0.00 0.00 40.92 2.97
491 492 8.844244 AGTGAGATTATCATTTTTGTCATAGCC 58.156 33.333 0.00 0.00 40.92 3.93
495 496 9.358406 AGATTATCATTTTTGTCATAGCCATCA 57.642 29.630 0.00 0.00 0.00 3.07
557 1589 1.285962 TCGGTGTACTTAGCCCTACCT 59.714 52.381 0.00 0.00 0.00 3.08
558 1590 2.509548 TCGGTGTACTTAGCCCTACCTA 59.490 50.000 0.00 0.00 0.00 3.08
574 1606 5.105716 CCCTACCTATCACTATGGACGAATG 60.106 48.000 0.00 0.00 0.00 2.67
602 1634 2.275134 TGCTTGATCTTGCCAGTTGA 57.725 45.000 7.77 0.00 0.00 3.18
622 1654 5.698741 TGACAAGTATTCATCCTCCACAT 57.301 39.130 0.00 0.00 0.00 3.21
623 1655 6.806668 TGACAAGTATTCATCCTCCACATA 57.193 37.500 0.00 0.00 0.00 2.29
625 1657 5.930135 ACAAGTATTCATCCTCCACATACC 58.070 41.667 0.00 0.00 0.00 2.73
627 1659 5.552870 AGTATTCATCCTCCACATACCAC 57.447 43.478 0.00 0.00 0.00 4.16
666 1698 2.883026 ACGATTTGATTTCCACCCCAA 58.117 42.857 0.00 0.00 0.00 4.12
667 1699 2.560981 ACGATTTGATTTCCACCCCAAC 59.439 45.455 0.00 0.00 0.00 3.77
688 1720 6.146673 CCAACGATTAATATTTCCCCGTAGTC 59.853 42.308 0.00 0.00 0.00 2.59
694 1729 1.843368 ATTTCCCCGTAGTCGACTCA 58.157 50.000 23.89 5.98 39.71 3.41
707 1749 2.163010 GTCGACTCACCACCGAAATCTA 59.837 50.000 8.70 0.00 33.91 1.98
709 1751 2.541556 GACTCACCACCGAAATCTAGC 58.458 52.381 0.00 0.00 0.00 3.42
718 1760 1.605712 CCGAAATCTAGCGATCCACCC 60.606 57.143 0.00 0.00 0.00 4.61
719 1761 1.784525 GAAATCTAGCGATCCACCCG 58.215 55.000 0.00 0.00 0.00 5.28
725 1767 1.046472 TAGCGATCCACCCGAACCAT 61.046 55.000 0.00 0.00 0.00 3.55
735 1777 3.085533 CACCCGAACCATAATCCACAAA 58.914 45.455 0.00 0.00 0.00 2.83
765 1807 1.133790 GACCATTGCTCCTGTGCATTC 59.866 52.381 0.00 0.00 42.96 2.67
813 1855 2.167662 CACTGGTGTCCATTTTACCCC 58.832 52.381 0.00 0.00 33.51 4.95
815 1857 2.167662 CTGGTGTCCATTTTACCCCAC 58.832 52.381 0.00 0.00 33.51 4.61
816 1858 1.783979 TGGTGTCCATTTTACCCCACT 59.216 47.619 0.00 0.00 33.51 4.00
868 1911 4.781959 CCCAATTGCTGCACGCCG 62.782 66.667 0.00 0.00 38.05 6.46
945 1992 3.120060 CCTACACATGAAAGAGCACAAGC 60.120 47.826 0.00 0.00 42.56 4.01
1227 2290 1.147473 CATTGCAAACCCTTTTCGGC 58.853 50.000 1.71 0.00 0.00 5.54
1230 2293 2.049526 CAAACCCTTTTCGGCGCC 60.050 61.111 19.07 19.07 0.00 6.53
1239 2302 4.644230 TTCGGCGCCGTGTACGTT 62.644 61.111 44.16 0.00 40.74 3.99
1540 2603 3.411808 GACGCCAATGTCGAGTACA 57.588 52.632 0.00 0.00 43.86 2.90
1584 2648 5.163764 GCATGCAAAAATTTAAGGGCTTACC 60.164 40.000 14.21 0.00 40.67 2.85
1602 2666 5.220854 GCTTACCGATTGTAATGCTTCACAT 60.221 40.000 0.00 0.00 42.30 3.21
1646 2710 9.679661 TCATTATTATTGCTTACTTCAGGTTGA 57.320 29.630 0.00 0.00 0.00 3.18
1758 2823 2.441750 ACCTAGGTGAAATGTGGTGTGT 59.558 45.455 15.42 0.00 0.00 3.72
1759 2824 2.813754 CCTAGGTGAAATGTGGTGTGTG 59.186 50.000 0.00 0.00 0.00 3.82
1855 2921 8.752005 ATTGCTTTATGACTTTATCCTTGCTA 57.248 30.769 0.00 0.00 0.00 3.49
1863 2929 3.385111 ACTTTATCCTTGCTACTCCCTCG 59.615 47.826 0.00 0.00 0.00 4.63
1867 2933 0.175989 CCTTGCTACTCCCTCGGTTC 59.824 60.000 0.00 0.00 0.00 3.62
1921 2987 5.648092 CGAACCAAGGGAATAGTTCAGAAAT 59.352 40.000 0.00 0.00 38.80 2.17
1965 3031 3.529533 AGAGATTGACTTCTTGCCATCG 58.470 45.455 0.00 0.00 0.00 3.84
1967 3033 2.012673 GATTGACTTCTTGCCATCGCT 58.987 47.619 0.00 0.00 35.36 4.93
1973 3039 1.741706 CTTCTTGCCATCGCTGATGTT 59.258 47.619 14.50 0.00 38.28 2.71
1978 3044 1.672363 TGCCATCGCTGATGTTGATTC 59.328 47.619 14.50 0.00 38.28 2.52
1998 3064 5.934935 TTCTTAAGTCGGTTTTAAGCTGG 57.065 39.130 1.63 0.00 37.79 4.85
1999 3065 4.964593 TCTTAAGTCGGTTTTAAGCTGGT 58.035 39.130 1.63 0.00 37.79 4.00
2005 3071 4.039703 GTCGGTTTTAAGCTGGTTTTCAC 58.960 43.478 0.00 0.00 0.00 3.18
2025 3091 4.686091 TCACTCAGTGCTATTTTTCACTCG 59.314 41.667 0.00 0.00 41.19 4.18
2089 3155 0.912486 ATGGGTCTTAGTGTGGAGCC 59.088 55.000 0.00 0.00 46.60 4.70
2099 3165 0.883833 GTGTGGAGCCCAAATGTCAG 59.116 55.000 0.00 0.00 34.18 3.51
2100 3166 0.770499 TGTGGAGCCCAAATGTCAGA 59.230 50.000 0.00 0.00 34.18 3.27
2148 3215 6.071447 CCCTCGAATCATGTCAGAGAAGATAT 60.071 42.308 10.24 0.00 0.00 1.63
2192 3262 5.658634 TGACTTGATCTTAGCACTATGACCT 59.341 40.000 0.00 0.00 0.00 3.85
2194 3264 5.423610 ACTTGATCTTAGCACTATGACCTGT 59.576 40.000 0.00 0.00 0.00 4.00
2199 3269 7.342026 TGATCTTAGCACTATGACCTGTTCTTA 59.658 37.037 0.00 0.00 0.00 2.10
2207 3277 7.965107 GCACTATGACCTGTTCTTAAGATTTTG 59.035 37.037 5.89 0.00 0.00 2.44
2244 3314 4.686396 GCTAAGACCCTTCCTTACAATCCC 60.686 50.000 0.00 0.00 0.00 3.85
2249 3319 2.422093 CCCTTCCTTACAATCCCTGAGC 60.422 54.545 0.00 0.00 0.00 4.26
2256 3326 4.503991 CCTTACAATCCCTGAGCATAGGTC 60.504 50.000 5.66 0.00 36.02 3.85
2299 3380 0.537143 TTGCAACATTGGAGACGCCT 60.537 50.000 0.00 0.00 37.63 5.52
2351 3433 5.939764 AGCATGACAAGAATGTAGTAGGA 57.060 39.130 0.00 0.00 40.74 2.94
2359 3441 9.653287 TGACAAGAATGTAGTAGGACAAATTAG 57.347 33.333 0.00 0.00 40.74 1.73
2361 3443 8.047310 ACAAGAATGTAGTAGGACAAATTAGGG 58.953 37.037 0.00 0.00 38.24 3.53
2363 3445 5.906772 ATGTAGTAGGACAAATTAGGGGG 57.093 43.478 0.00 0.00 31.83 5.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 4.321601 CCAACTGTATGATTCCCGCAAAAA 60.322 41.667 0.00 0.00 0.00 1.94
17 18 3.192422 CCAACTGTATGATTCCCGCAAAA 59.808 43.478 0.00 0.00 0.00 2.44
18 19 2.752354 CCAACTGTATGATTCCCGCAAA 59.248 45.455 0.00 0.00 0.00 3.68
19 20 2.364632 CCAACTGTATGATTCCCGCAA 58.635 47.619 0.00 0.00 0.00 4.85
20 21 1.408127 CCCAACTGTATGATTCCCGCA 60.408 52.381 0.00 0.00 0.00 5.69
21 22 1.308998 CCCAACTGTATGATTCCCGC 58.691 55.000 0.00 0.00 0.00 6.13
22 23 1.211949 ACCCCAACTGTATGATTCCCG 59.788 52.381 0.00 0.00 0.00 5.14
23 24 3.288092 GAACCCCAACTGTATGATTCCC 58.712 50.000 0.00 0.00 0.00 3.97
24 25 2.943033 CGAACCCCAACTGTATGATTCC 59.057 50.000 0.00 0.00 0.00 3.01
25 26 3.869065 TCGAACCCCAACTGTATGATTC 58.131 45.455 0.00 0.00 0.00 2.52
26 27 3.992943 TCGAACCCCAACTGTATGATT 57.007 42.857 0.00 0.00 0.00 2.57
27 28 5.623956 TTATCGAACCCCAACTGTATGAT 57.376 39.130 0.00 0.00 0.00 2.45
55 56 5.163982 GCTCTGAGATGTAAACAAACGGTAC 60.164 44.000 9.28 0.00 0.00 3.34
81 82 1.192146 TGTTCGGTTGGAGCTAGGCT 61.192 55.000 0.00 0.00 43.88 4.58
88 89 1.065491 TCCATGGATGTTCGGTTGGAG 60.065 52.381 11.44 0.00 0.00 3.86
92 93 4.718940 GAAAATCCATGGATGTTCGGTT 57.281 40.909 32.53 18.63 38.57 4.44
121 122 2.310647 ACCGTTCAATTTCCATAGGGGT 59.689 45.455 0.00 0.00 38.11 4.95
122 123 3.012934 ACCGTTCAATTTCCATAGGGG 57.987 47.619 0.00 0.00 38.37 4.79
123 124 5.400066 AAAACCGTTCAATTTCCATAGGG 57.600 39.130 0.00 0.00 0.00 3.53
130 131 4.927422 TCACAGGAAAACCGTTCAATTTC 58.073 39.130 0.00 0.00 33.38 2.17
131 132 4.993029 TCACAGGAAAACCGTTCAATTT 57.007 36.364 0.00 0.00 0.00 1.82
132 133 4.993029 TTCACAGGAAAACCGTTCAATT 57.007 36.364 0.00 0.00 0.00 2.32
133 134 4.158764 TGTTTCACAGGAAAACCGTTCAAT 59.841 37.500 0.00 0.00 44.18 2.57
134 135 3.506455 TGTTTCACAGGAAAACCGTTCAA 59.494 39.130 0.00 0.00 44.18 2.69
135 136 3.082548 TGTTTCACAGGAAAACCGTTCA 58.917 40.909 0.00 0.00 44.18 3.18
136 137 3.431856 GTGTTTCACAGGAAAACCGTTC 58.568 45.455 0.00 0.00 44.18 3.95
137 138 2.164827 GGTGTTTCACAGGAAAACCGTT 59.835 45.455 2.41 0.00 44.18 4.44
138 139 1.746787 GGTGTTTCACAGGAAAACCGT 59.253 47.619 2.41 0.00 44.18 4.83
139 140 1.066454 GGGTGTTTCACAGGAAAACCG 59.934 52.381 2.41 0.00 44.18 4.44
140 141 1.066454 CGGGTGTTTCACAGGAAAACC 59.934 52.381 2.41 0.00 44.18 3.27
141 142 1.066454 CCGGGTGTTTCACAGGAAAAC 59.934 52.381 0.00 0.00 44.18 2.43
142 143 1.394618 CCGGGTGTTTCACAGGAAAA 58.605 50.000 0.00 0.00 44.18 2.29
143 144 0.466555 CCCGGGTGTTTCACAGGAAA 60.467 55.000 14.18 0.00 40.60 3.13
144 145 1.149627 CCCGGGTGTTTCACAGGAA 59.850 57.895 14.18 0.00 36.36 3.36
145 146 2.824880 CCCCGGGTGTTTCACAGGA 61.825 63.158 21.85 0.00 36.36 3.86
146 147 2.282180 CCCCGGGTGTTTCACAGG 60.282 66.667 21.85 0.00 35.86 4.00
147 148 2.983592 GCCCCGGGTGTTTCACAG 60.984 66.667 21.85 0.73 35.86 3.66
148 149 3.810188 TGCCCCGGGTGTTTCACA 61.810 61.111 21.85 2.61 35.86 3.58
149 150 3.292159 GTGCCCCGGGTGTTTCAC 61.292 66.667 21.85 14.58 0.00 3.18
150 151 4.589675 GGTGCCCCGGGTGTTTCA 62.590 66.667 21.85 6.13 0.00 2.69
196 197 3.000727 GAGGAGTAACAAATGGTCCACG 58.999 50.000 0.00 0.00 0.00 4.94
206 207 2.496070 CTCCGGACATGAGGAGTAACAA 59.504 50.000 20.54 0.00 46.68 2.83
213 214 4.030913 AGTAAAATCTCCGGACATGAGGA 58.969 43.478 0.00 4.40 34.93 3.71
214 215 4.408182 AGTAAAATCTCCGGACATGAGG 57.592 45.455 0.00 0.00 0.00 3.86
215 216 7.041780 CCATAAAGTAAAATCTCCGGACATGAG 60.042 40.741 0.00 0.00 0.00 2.90
216 217 6.765989 CCATAAAGTAAAATCTCCGGACATGA 59.234 38.462 0.00 0.00 0.00 3.07
217 218 6.513393 GCCATAAAGTAAAATCTCCGGACATG 60.513 42.308 0.00 0.00 0.00 3.21
218 219 5.531287 GCCATAAAGTAAAATCTCCGGACAT 59.469 40.000 0.00 0.00 0.00 3.06
219 220 4.879545 GCCATAAAGTAAAATCTCCGGACA 59.120 41.667 0.00 0.00 0.00 4.02
220 221 4.275196 GGCCATAAAGTAAAATCTCCGGAC 59.725 45.833 0.00 0.00 0.00 4.79
221 222 4.165372 AGGCCATAAAGTAAAATCTCCGGA 59.835 41.667 5.01 2.93 0.00 5.14
222 223 4.461198 AGGCCATAAAGTAAAATCTCCGG 58.539 43.478 5.01 0.00 0.00 5.14
223 224 7.562454 TTTAGGCCATAAAGTAAAATCTCCG 57.438 36.000 5.01 0.00 0.00 4.63
224 225 9.750125 CATTTTAGGCCATAAAGTAAAATCTCC 57.250 33.333 5.01 0.00 34.39 3.71
229 230 8.032451 GCTGACATTTTAGGCCATAAAGTAAAA 58.968 33.333 5.01 6.66 34.86 1.52
230 231 7.177568 TGCTGACATTTTAGGCCATAAAGTAAA 59.822 33.333 5.01 0.00 34.86 2.01
231 232 6.661377 TGCTGACATTTTAGGCCATAAAGTAA 59.339 34.615 5.01 0.00 34.86 2.24
232 233 6.184068 TGCTGACATTTTAGGCCATAAAGTA 58.816 36.000 5.01 0.00 34.86 2.24
233 234 5.016173 TGCTGACATTTTAGGCCATAAAGT 58.984 37.500 5.01 5.13 34.86 2.66
234 235 5.581126 TGCTGACATTTTAGGCCATAAAG 57.419 39.130 5.01 2.05 34.86 1.85
235 236 5.991933 TTGCTGACATTTTAGGCCATAAA 57.008 34.783 5.01 4.97 0.00 1.40
236 237 5.991933 TTTGCTGACATTTTAGGCCATAA 57.008 34.783 5.01 0.00 0.00 1.90
237 238 5.068987 GGATTTGCTGACATTTTAGGCCATA 59.931 40.000 5.01 0.00 0.00 2.74
238 239 4.141869 GGATTTGCTGACATTTTAGGCCAT 60.142 41.667 5.01 0.00 0.00 4.40
239 240 3.195396 GGATTTGCTGACATTTTAGGCCA 59.805 43.478 5.01 0.00 0.00 5.36
263 264 3.116300 GACGTATGACTAGTGTGCATGG 58.884 50.000 0.00 0.00 0.00 3.66
286 287 3.399440 TTTTTAGGGGAACGAGCGTTA 57.601 42.857 8.37 0.00 38.60 3.18
312 313 2.889045 CCATTGGACCTGGAGCATTATG 59.111 50.000 0.00 0.00 35.70 1.90
317 318 1.367346 TTACCATTGGACCTGGAGCA 58.633 50.000 10.37 0.00 37.22 4.26
339 340 2.032377 GGCGCGCAATATTAAGTAAGCA 60.032 45.455 34.42 0.00 0.00 3.91
353 354 1.237533 AATGATAATCATGGCGCGCA 58.762 45.000 34.42 19.50 37.15 6.09
378 379 9.379791 CGATACAAAATAAAGAAGTAACCCTCT 57.620 33.333 0.00 0.00 0.00 3.69
379 380 9.159364 ACGATACAAAATAAAGAAGTAACCCTC 57.841 33.333 0.00 0.00 0.00 4.30
380 381 9.511272 AACGATACAAAATAAAGAAGTAACCCT 57.489 29.630 0.00 0.00 0.00 4.34
381 382 9.764870 GAACGATACAAAATAAAGAAGTAACCC 57.235 33.333 0.00 0.00 0.00 4.11
382 383 9.469239 CGAACGATACAAAATAAAGAAGTAACC 57.531 33.333 0.00 0.00 0.00 2.85
383 384 9.469239 CCGAACGATACAAAATAAAGAAGTAAC 57.531 33.333 0.00 0.00 0.00 2.50
384 385 8.170553 GCCGAACGATACAAAATAAAGAAGTAA 58.829 33.333 0.00 0.00 0.00 2.24
385 386 7.201548 GGCCGAACGATACAAAATAAAGAAGTA 60.202 37.037 0.00 0.00 0.00 2.24
386 387 6.402875 GGCCGAACGATACAAAATAAAGAAGT 60.403 38.462 0.00 0.00 0.00 3.01
387 388 5.963586 GGCCGAACGATACAAAATAAAGAAG 59.036 40.000 0.00 0.00 0.00 2.85
388 389 5.446206 CGGCCGAACGATACAAAATAAAGAA 60.446 40.000 24.07 0.00 35.47 2.52
389 390 4.033129 CGGCCGAACGATACAAAATAAAGA 59.967 41.667 24.07 0.00 35.47 2.52
390 391 4.201744 ACGGCCGAACGATACAAAATAAAG 60.202 41.667 35.90 0.00 37.61 1.85
391 392 3.683822 ACGGCCGAACGATACAAAATAAA 59.316 39.130 35.90 0.00 37.61 1.40
392 393 3.062369 CACGGCCGAACGATACAAAATAA 59.938 43.478 35.90 0.00 37.61 1.40
393 394 2.604011 CACGGCCGAACGATACAAAATA 59.396 45.455 35.90 0.00 37.61 1.40
394 395 1.395608 CACGGCCGAACGATACAAAAT 59.604 47.619 35.90 0.00 37.61 1.82
395 396 0.791422 CACGGCCGAACGATACAAAA 59.209 50.000 35.90 0.00 37.61 2.44
396 397 0.319727 ACACGGCCGAACGATACAAA 60.320 50.000 35.90 0.00 37.61 2.83
397 398 0.525311 TACACGGCCGAACGATACAA 59.475 50.000 35.90 3.03 37.61 2.41
398 399 0.740149 ATACACGGCCGAACGATACA 59.260 50.000 35.90 7.77 37.61 2.29
399 400 1.843992 AATACACGGCCGAACGATAC 58.156 50.000 35.90 0.00 37.61 2.24
400 401 2.582728 AAATACACGGCCGAACGATA 57.417 45.000 35.90 15.96 37.61 2.92
401 402 1.395608 CAAAATACACGGCCGAACGAT 59.604 47.619 35.90 16.19 37.61 3.73
402 403 0.791422 CAAAATACACGGCCGAACGA 59.209 50.000 35.90 14.43 37.61 3.85
403 404 0.791422 TCAAAATACACGGCCGAACG 59.209 50.000 35.90 21.75 40.31 3.95
404 405 3.168193 CAATCAAAATACACGGCCGAAC 58.832 45.455 35.90 0.00 0.00 3.95
405 406 2.814919 ACAATCAAAATACACGGCCGAA 59.185 40.909 35.90 17.45 0.00 4.30
406 407 2.428491 ACAATCAAAATACACGGCCGA 58.572 42.857 35.90 10.61 0.00 5.54
407 408 2.911819 ACAATCAAAATACACGGCCG 57.088 45.000 26.86 26.86 0.00 6.13
408 409 3.908213 ACAACAATCAAAATACACGGCC 58.092 40.909 0.00 0.00 0.00 6.13
409 410 5.898630 AAACAACAATCAAAATACACGGC 57.101 34.783 0.00 0.00 0.00 5.68
410 411 9.405587 AGATAAAACAACAATCAAAATACACGG 57.594 29.630 0.00 0.00 0.00 4.94
419 420 9.781834 CCGCTTTATAGATAAAACAACAATCAA 57.218 29.630 0.00 0.00 32.39 2.57
420 421 8.402472 CCCGCTTTATAGATAAAACAACAATCA 58.598 33.333 0.00 0.00 32.39 2.57
421 422 7.860872 CCCCGCTTTATAGATAAAACAACAATC 59.139 37.037 0.00 0.00 32.39 2.67
422 423 7.683463 GCCCCGCTTTATAGATAAAACAACAAT 60.683 37.037 0.00 0.00 32.39 2.71
423 424 6.404954 GCCCCGCTTTATAGATAAAACAACAA 60.405 38.462 0.00 0.00 32.39 2.83
424 425 5.066764 GCCCCGCTTTATAGATAAAACAACA 59.933 40.000 0.00 0.00 32.39 3.33
425 426 5.516996 GCCCCGCTTTATAGATAAAACAAC 58.483 41.667 0.00 0.00 32.39 3.32
426 427 4.273969 CGCCCCGCTTTATAGATAAAACAA 59.726 41.667 0.00 0.00 32.39 2.83
427 428 3.810941 CGCCCCGCTTTATAGATAAAACA 59.189 43.478 0.00 0.00 32.39 2.83
428 429 4.400036 CGCCCCGCTTTATAGATAAAAC 57.600 45.455 0.00 0.00 32.39 2.43
447 448 3.843240 CTCGAAACAGGCTCGCGC 61.843 66.667 0.00 0.00 36.25 6.86
448 449 2.126463 TCTCGAAACAGGCTCGCG 60.126 61.111 0.00 0.00 36.25 5.87
449 450 1.080434 ACTCTCGAAACAGGCTCGC 60.080 57.895 0.00 0.00 36.25 5.03
450 451 0.241213 TCACTCTCGAAACAGGCTCG 59.759 55.000 0.00 0.00 37.66 5.03
451 452 1.542030 TCTCACTCTCGAAACAGGCTC 59.458 52.381 0.00 0.00 0.00 4.70
452 453 1.621992 TCTCACTCTCGAAACAGGCT 58.378 50.000 0.00 0.00 0.00 4.58
453 454 2.663826 ATCTCACTCTCGAAACAGGC 57.336 50.000 0.00 0.00 0.00 4.85
454 455 5.895928 TGATAATCTCACTCTCGAAACAGG 58.104 41.667 0.00 0.00 0.00 4.00
455 456 8.417780 AAATGATAATCTCACTCTCGAAACAG 57.582 34.615 0.00 0.00 36.48 3.16
456 457 8.777865 AAAATGATAATCTCACTCTCGAAACA 57.222 30.769 0.00 0.00 36.48 2.83
457 458 9.483062 CAAAAATGATAATCTCACTCTCGAAAC 57.517 33.333 0.00 0.00 36.48 2.78
458 459 9.219603 ACAAAAATGATAATCTCACTCTCGAAA 57.780 29.630 0.00 0.00 36.48 3.46
459 460 8.777865 ACAAAAATGATAATCTCACTCTCGAA 57.222 30.769 0.00 0.00 36.48 3.71
460 461 8.034804 TGACAAAAATGATAATCTCACTCTCGA 58.965 33.333 0.00 0.00 36.48 4.04
461 462 8.189709 TGACAAAAATGATAATCTCACTCTCG 57.810 34.615 0.00 0.00 36.48 4.04
464 465 9.875675 GCTATGACAAAAATGATAATCTCACTC 57.124 33.333 0.00 0.00 36.48 3.51
465 466 8.844244 GGCTATGACAAAAATGATAATCTCACT 58.156 33.333 0.00 0.00 36.48 3.41
466 467 8.623903 TGGCTATGACAAAAATGATAATCTCAC 58.376 33.333 0.00 0.00 36.48 3.51
467 468 8.750515 TGGCTATGACAAAAATGATAATCTCA 57.249 30.769 0.00 0.00 38.53 3.27
468 469 9.837525 GATGGCTATGACAAAAATGATAATCTC 57.162 33.333 0.00 0.00 0.00 2.75
469 470 9.358406 TGATGGCTATGACAAAAATGATAATCT 57.642 29.630 0.00 0.00 0.00 2.40
470 471 9.970395 TTGATGGCTATGACAAAAATGATAATC 57.030 29.630 0.00 0.00 0.00 1.75
490 491 9.511272 TTGAGATTCCACTGATTATATTGATGG 57.489 33.333 0.00 0.00 0.00 3.51
537 538 1.285962 AGGTAGGGCTAAGTACACCGA 59.714 52.381 0.00 0.00 0.00 4.69
538 539 1.772836 AGGTAGGGCTAAGTACACCG 58.227 55.000 0.00 0.00 0.00 4.94
557 1589 4.820897 GATGGCATTCGTCCATAGTGATA 58.179 43.478 0.00 0.00 43.90 2.15
558 1590 3.668447 GATGGCATTCGTCCATAGTGAT 58.332 45.455 0.00 0.00 43.90 3.06
574 1606 2.228343 GCAAGATCAAGCATAGGATGGC 59.772 50.000 0.00 0.00 0.00 4.40
602 1634 5.428457 TGGTATGTGGAGGATGAATACTTGT 59.572 40.000 0.00 0.00 0.00 3.16
627 1659 2.079925 GTTAAAGCCTCACAGCCTCTG 58.920 52.381 0.00 0.00 37.52 3.35
666 1698 5.241506 TCGACTACGGGGAAATATTAATCGT 59.758 40.000 0.00 0.00 40.21 3.73
667 1699 5.570589 GTCGACTACGGGGAAATATTAATCG 59.429 44.000 8.70 0.00 40.21 3.34
688 1720 2.798680 CTAGATTTCGGTGGTGAGTCG 58.201 52.381 0.00 0.00 0.00 4.18
694 1729 1.068741 GGATCGCTAGATTTCGGTGGT 59.931 52.381 0.00 0.00 37.19 4.16
707 1749 1.046472 TATGGTTCGGGTGGATCGCT 61.046 55.000 0.00 0.00 0.00 4.93
709 1751 2.413837 GATTATGGTTCGGGTGGATCG 58.586 52.381 0.00 0.00 0.00 3.69
718 1760 7.702386 TGATGTTATTTGTGGATTATGGTTCG 58.298 34.615 0.00 0.00 0.00 3.95
719 1761 9.467258 CATGATGTTATTTGTGGATTATGGTTC 57.533 33.333 0.00 0.00 0.00 3.62
725 1767 8.765488 ATGGTCATGATGTTATTTGTGGATTA 57.235 30.769 0.00 0.00 0.00 1.75
735 1777 4.825634 CAGGAGCAATGGTCATGATGTTAT 59.174 41.667 20.51 0.00 43.12 1.89
765 1807 0.605860 GATATGCAGCTGGGGAGCAG 60.606 60.000 17.12 0.00 42.14 4.24
945 1992 1.268625 TGCTACTACGTGTGTCTGTGG 59.731 52.381 0.00 0.00 0.00 4.17
1050 2104 1.443407 CCTATGGGCCTCACTCACG 59.557 63.158 4.53 0.00 0.00 4.35
1227 2290 1.465991 CGTCCATAACGTACACGGCG 61.466 60.000 4.80 4.80 46.42 6.46
1239 2302 2.767445 CGTCAGCGGGTCGTCCATA 61.767 63.158 0.04 0.00 34.36 2.74
1303 2366 0.757935 TGGTCCGCCCCTATGTAGAC 60.758 60.000 0.00 0.00 0.00 2.59
1431 2494 2.910360 CCGGTGATGGGCATCTCA 59.090 61.111 0.00 0.00 38.60 3.27
1501 2564 1.605058 CCGGTCTTGAGGTCCATCGT 61.605 60.000 0.00 0.00 0.00 3.73
1540 2603 5.559427 TGCTAATGCATGACATAAACGTT 57.441 34.783 0.00 0.00 45.31 3.99
1569 2632 7.683463 GCATTACAATCGGTAAGCCCTTAAATT 60.683 37.037 0.00 0.00 44.74 1.82
1584 2648 6.349973 ACACTATGTGAAGCATTACAATCG 57.650 37.500 4.61 0.00 38.94 3.34
1625 2689 5.938125 ACGTCAACCTGAAGTAAGCAATAAT 59.062 36.000 0.00 0.00 37.33 1.28
1646 2710 2.851195 AGTCCAAATCTCAAAGCACGT 58.149 42.857 0.00 0.00 0.00 4.49
1686 2751 0.687427 AACCCAAGCAAAGGCACACT 60.687 50.000 0.00 0.00 44.61 3.55
1855 2921 5.247792 ACACTTAATTTAGAACCGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
1863 2929 6.663944 ATCAGCGACACTTAATTTAGAACC 57.336 37.500 0.00 0.00 0.00 3.62
1897 2963 4.202245 TCTGAACTATTCCCTTGGTTCG 57.798 45.455 0.00 0.00 40.34 3.95
1939 3005 3.126686 GGCAAGAAGTCAATCTCTTCAGC 59.873 47.826 8.10 10.08 42.35 4.26
1965 3031 4.631813 ACCGACTTAAGAATCAACATCAGC 59.368 41.667 10.09 0.00 0.00 4.26
1967 3033 7.504924 AAAACCGACTTAAGAATCAACATCA 57.495 32.000 10.09 0.00 0.00 3.07
1973 3039 6.148811 CCAGCTTAAAACCGACTTAAGAATCA 59.851 38.462 10.09 0.00 38.21 2.57
1978 3044 5.684550 AACCAGCTTAAAACCGACTTAAG 57.315 39.130 0.00 0.00 38.73 1.85
1998 3064 7.196331 AGTGAAAAATAGCACTGAGTGAAAAC 58.804 34.615 18.18 0.00 43.26 2.43
1999 3065 7.333528 AGTGAAAAATAGCACTGAGTGAAAA 57.666 32.000 18.18 0.22 43.26 2.29
2005 3071 3.997021 ACCGAGTGAAAAATAGCACTGAG 59.003 43.478 0.00 0.00 44.77 3.35
2039 3105 6.757897 TTAAACATTGGAGGAATGCTAGTG 57.242 37.500 0.00 0.00 44.85 2.74
2157 3224 9.770097 TGCTAAGATCAAGTCATAAGGAATAAG 57.230 33.333 0.00 0.00 0.00 1.73
2211 3281 4.100344 GGAAGGGTCTTAGCAAAAACCAAA 59.900 41.667 0.00 0.00 33.27 3.28
2215 3285 5.533528 TGTAAGGAAGGGTCTTAGCAAAAAC 59.466 40.000 0.00 0.00 0.00 2.43
2249 3319 8.463930 TCCCAAAAATAGCATTAAGACCTATG 57.536 34.615 0.00 0.00 0.00 2.23
2256 3326 9.090692 CAAAGACATCCCAAAAATAGCATTAAG 57.909 33.333 0.00 0.00 0.00 1.85
2299 3380 3.075582 AGGTAGAGTGAACTAGTGACCCA 59.924 47.826 0.00 0.00 0.00 4.51
2339 3421 6.296803 CCCCCTAATTTGTCCTACTACATTC 58.703 44.000 0.00 0.00 0.00 2.67
2361 3443 2.671963 GACCAAACGTCTGCCCCC 60.672 66.667 0.00 0.00 38.57 5.40
2519 3614 8.417780 TCACACTATTTTGACCAAAACATTTG 57.582 30.769 9.75 7.79 42.32 2.32
2528 3623 8.862325 AGTCATTATTCACACTATTTTGACCA 57.138 30.769 0.00 0.00 33.24 4.02


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.